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Crystal structure of GAD1 from arabidopsis thaliana

Analyse Crystal structure of GAD1 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HBX
Type: protein
Length: 2,620 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate decarboxylase 1
EC: 4.1.1.15
UniProt: Q42521
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F	Glutamate decarboxylase 1 (EC 4.1.1.15)	protein	437	41% helix, 16% strand	Q42521
D, E	Glutamate decarboxylase 1 (EC 4.1.1.15)	protein	436	41% helix, 16% strand	Q42521

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.79	0.84	74	empty
2	612	0.77	0.83	71	empty
3	548	0.77	0.84	67	empty
4	437	0.75	0.84	61	empty
5	85	0.74	0.97	27	empty

Interfaces

12 interfaces between chains.

A–B · 5463 Å² buried · 82 hydrogen bonds · protein-protein
E–F · 5449 Å² buried · 76 hydrogen bonds · protein-protein
C–D · 5387 Å² buried · 79 hydrogen bonds · protein-protein
B–C · 2251 Å² buried · 35 hydrogen bonds · protein-protein
A–F · 2237 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (cofactor).

Compared structures

3HBX · Crystal structure of GAD1 from Arabidopsis thaliana · the same entry in another collection · chain F against F, TM-score 1.00
Q42521 · AlphaFold monomer V2.0 prediction for glutamate decarboxylase 1 (Q42521) · a predicted model of the same protein · chain E against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q42521
Elsewhere: RCSB PDB 3HBX · PDBe 3HBX · UniProt Q42521

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